GLNB - ECOLI - GREMLIN Contacts

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GLNB - Nitrogen regulatory protein P-II 1

UniProt:	P0A9Z1	Sequences: MKKIDAIIKPFKLDDVREALAEVGITGMTVTEVKGFGRQKGHTELYRGAEYMVDFLPKVKIEIVVPDDIVDTCVDTIIRTAQTGKIGDGKIFVFDVARVIRIRTGEEDDAAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10384
Length:	112 (112)
Sequences:	2943 (1586)
Seq/√Len:	149.9

ECOLI - GLNB GLNK
BACSU - NRGB

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_R	107_E	4.434	1.00
64_V	96_V	3.665	1.00
98_R	108_D	3.594	1.00
65_V	73_C	3.046	1.00
66_P	109_D	2.626	1.00
12_K	15_D	2.497	1.00
69_I	72_T	2.393	1.00
16_V	81_A	2.258	1.00
78_I	82_Q	2.245	1.00
6_A	77_I	2.228	1.00
23_V	76_T	2.181	1.00
29_T	33_V	2.165	1.00
5_D	94_F	1.960	1.00
76_T	80_T	1.934	1.00
75_D	79_R	1.899	1.00
74_V	93_V	1.834	1.00
66_P	69_I	1.793	1.00
3_K	64_V	1.694	1.00
71_D	75_D	1.682	1.00
8_I	16_V	1.664	1.00
13_L	30_V	1.557	1.00
31_T	62_E	1.497	1.00
16_V	61_I	1.394	1.00
72_T	76_T	1.370	1.00
31_T	60_K	1.347	1.00
4_I	73_C	1.344	1.00
67_D	109_D	1.309	1.00
74_V	91_I	1.269	1.00
2_K	67_D	1.263	1.00
75_D	78_I	1.254	1.00
78_I	91_I	1.228	1.00
3_K	94_F	1.213	1.00
18_E	22_E	1.212	1.00
78_I	107_E	1.203	1.00
5_D	60_K	1.170	1.00
4_I	65_V	1.164	1.00
72_T	79_R	1.161	1.00
8_I	61_I	1.161	1.00
19_A	22_E	1.158	1.00
101_R	106_E	1.146	1.00
7_I	29_T	1.135	1.00
19_A	79_R	1.120	0.99
65_V	70_V	1.115	0.99
71_D	107_E	1.108	0.99
82_Q	105_G	1.105	0.99
30_V	55_F	1.104	0.99
2_K	95_D	1.101	0.99
64_V	92_F	1.099	0.99
8_I	13_L	1.098	0.99
17_R	28_M	1.094	0.99
9_K	86_I	1.094	0.99
2_K	70_V	1.088	0.99
39_Q	56_L	1.087	0.99
92_F	102_I	1.074	0.99
2_K	93_V	1.058	0.99
71_D	98_R	1.057	0.99
70_V	74_V	1.057	0.99
5_D	64_V	1.043	0.99
78_I	100_I	1.034	0.99
2_K	97_A	1.029	0.99
39_Q	58_K	1.020	0.99
103_R	106_E	1.011	0.99
19_A	80_T	1.002	0.99
13_L	59_V	0.984	0.99
84_G	88_D	0.974	0.99
20_L	63_I	0.967	0.98
72_T	75_D	0.947	0.98
21_A	36_F	0.939	0.98
9_K	33_V	0.936	0.98
42_H	54_D	0.933	0.98
4_I	77_I	0.927	0.98
36_F	54_D	0.905	0.98
25_I	63_I	0.904	0.98
36_F	42_H	0.898	0.97
63_I	73_C	0.896	0.97
23_V	72_T	0.895	0.97
99_V	111_A	0.885	0.97
83_T	88_D	0.866	0.97
19_A	76_T	0.856	0.97
69_I	73_C	0.845	0.96
27_G	36_F	0.815	0.96
16_V	80_T	0.788	0.95
60_K	92_F	0.781	0.94
43_T	50_E	0.779	0.94
100_I	107_E	0.775	0.94
46_Y	49_A	0.771	0.94
7_I	92_F	0.767	0.94
74_V	100_I	0.751	0.93
13_L	54_D	0.751	0.93
41_G	58_K	0.745	0.93
42_H	49_A	0.738	0.93
36_F	55_F	0.733	0.92
11_F	15_D	0.732	0.92
6_A	81_A	0.731	0.92
47_R	51_Y	0.730	0.92
20_L	77_I	0.727	0.92
45_L	49_A	0.726	0.92
42_H	45_L	0.721	0.92
28_M	61_I	0.720	0.92
6_A	63_I	0.710	0.91
3_K	96_V	0.694	0.90
42_H	50_E	0.691	0.90
25_I	73_C	0.680	0.89
8_I	77_I	0.672	0.89
5_D	62_E	0.669	0.88
21_A	40_K	0.666	0.88
48_G	51_Y	0.665	0.88
13_L	55_F	0.661	0.88
37_G	90_K	0.656	0.87
11_F	56_L	0.653	0.87
92_F	99_V	0.651	0.87
70_V	95_D	0.650	0.87
20_L	73_C	0.649	0.87
66_P	73_C	0.648	0.87
45_L	85_K	0.648	0.87
33_V	60_K	0.644	0.86
91_I	100_I	0.628	0.85
8_I	12_K	0.627	0.85
67_D	70_V	0.627	0.85
15_D	80_T	0.626	0.85
45_L	50_E	0.613	0.84
43_T	52_M	0.608	0.83
1_M	67_D	0.604	0.83
30_V	61_I	0.593	0.82
41_G	44_E	0.591	0.81
3_K	92_F	0.591	0.81
5_D	99_V	0.591	0.81
32_E	59_V	0.589	0.81
34_K	46_Y	0.588	0.81
71_D	78_I	0.586	0.81
79_R	82_Q	0.585	0.81
17_R	21_A	0.582	0.80
20_L	61_I	0.579	0.80
17_R	54_D	0.577	0.80
27_G	99_V	0.573	0.79
22_E	79_R	0.571	0.79
38_R	44_E	0.570	0.79
44_E	49_A	0.567	0.79
57_P	85_K	0.562	0.78
11_F	55_F	0.561	0.78
25_I	42_H	0.560	0.78
20_L	72_T	0.552	0.77
36_F	102_I	0.550	0.77
27_G	56_L	0.547	0.76
45_L	54_D	0.546	0.76
28_M	62_E	0.542	0.75
76_T	79_R	0.540	0.75
39_Q	86_I	0.538	0.75
11_F	32_E	0.535	0.75
70_V	98_R	0.534	0.74
28_M	52_M	0.532	0.74
38_R	102_I	0.528	0.74
9_K	82_Q	0.528	0.74
48_G	62_E	0.527	0.73
11_F	49_A	0.523	0.73
25_I	76_T	0.521	0.73
77_I	81_A	0.518	0.72
74_V	78_I	0.518	0.72
13_L	61_I	0.515	0.72
70_V	93_V	0.515	0.72
13_L	52_M	0.514	0.72
42_H	85_K	0.513	0.71
53_V	112_I	0.513	0.71
2_K	8_I	0.511	0.71
20_L	23_V	0.504	0.70
100_I	106_E	0.500	0.70
85_K	102_I	0.500	0.70
13_L	28_M	0.500	0.70

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4ozjA	3	0.875	100	0.18	Contact Map
3t9zA	3	0.875	100	0.191	Contact Map
2o66A	5	0.8661	100	0.193	Contact Map
3ncqA	4	1	100	0.199	Contact Map
1hwuA	6	0.9554	100	0.209	Contact Map
1vfjA	3	1	100	0.212	Contact Map
4r25A	3	1	100	0.214	Contact Map
3bzqA	3	0.8661	100	0.214	Contact Map
3l7pA	4	0.8125	100	0.216	Contact Map
2ns1B	3	1	100	0.225	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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